[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 11 11:52:42 CEST 2013 

Don't know, sorry. None of the devs use Cygwin. I suggest you follow
the normal instructions to install FFTW manually, and then direct
CMake to use it.

Mark

On Wed, Sep 11, 2013 at 9:38 AM, shahid nayeem <msnayeem at gmail.com> wrote:
> Thanks Mark
>
> $ make
> [  0%] Built target gmxfftw
> make[2]: *** No rule to make target
> `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
> needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
> CMakeFiles/Makefile2:1238: recipe for target
> `src/gmxlib/CMakeFiles/gmx.dir/all' failed
> make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> Makefile:146: recipe for target `all' failed
> make: *** [all] Error 2
>
> I checked in folder
> /cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
> , this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
> locate it.
> Please help me
>
> shahid Nayeem
>
>
> On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem <msnayeem at gmail.com> wrote:
>
>> Thanks. But when I ran make again I am getting this error
>> [  0%] Built target gmxfftw
>> make[2]: *** No rule to make target
>> `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
>> needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
>> CMakeFiles/Makefile2:1238: recipe for target
>> `src/gmxlib/CMakeFiles/gmx.dir/all' failed
>> make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
>> Makefile:146: recipe for target `all' failed
>> make: *** [all] Error 2
>>  shahid Nayeem
>>
>>
>> On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>>
>>> For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
>>> this problem. Run make a second time and it will work.
>>>
>>> Mark
>>>
>>> On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem <msnayeem at gmail.com>
>>> wrote:
>>> > Thanks Wahab
>>> > I followed your instruction and added  #define HAVE_SYS_TIME_H
>>> >
>>> > at the very top of the file gmxlib/thread_mpi/impl.h.
>>> > Then again in make command I got following errors.
>>> > [ 53%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
>>> > [ 53%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
>>> > [ 53%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
>>> > [ 53%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
>>> > [ 53%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
>>> > [ 55%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
>>> > [ 56%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
>>> > [ 56%] Building C object
>>> >
>>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
>>> > make[2]: *** No rule to make target
>>> >
>>> `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
>>> > needed by `src/gmxlib/cyggmx_d-8.dll'.  Stop.
>>> > CMakeFiles/Makefile2:1238: recipe for target
>>> > `src/gmxlib/CMakeFiles/gmx.dir/all' failed
>>> > make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
>>> > Makefile:146: recipe for target `all' failed
>>> > make: *** [all] Error 2
>>> >
>>> > Please help me to compile gromacs 4.6.3 on cygwin
>>> >
>>> > Shahid Nayeem
>>> >
>>> >
>>> > On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab <
>>> > mirco.wahab at chemie.tu-freiberg.de> wrote:
>>> >
>>> >> On 10.09.2013 08:20, shahid nayeem wrote:
>>> >>
>>> >>> I am installing gromacs -4.6.3 on cygwin with following commands
>>> >>> tar -xvzf gramcs-4.6.3.tar.gz
>>> >>> cd gromacs-4.6.3
>>> >>> mkdir build
>>> >>> cd build
>>> >>>   cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
>>> >>> It runs fine and write file in build directory.
>>> >>> when I run make command it gives following error.
>>> >>> ...
>>> >>>
>>> >>> /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/**
>>> >>> impl.h:504:20:
>>> >>> error: field ‘timer_init’ has incomplete type
>>> >>>       struct timeval timer_init;
>>> >>>                      ^
>>> >>> src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target
>>> >>>
>>> >>
>>> >> The Gromacs-file "gmxlib/thread_mpi/impl.h" is missing the
>>> >> correct #define for the "unixish" Cygwin pseudo-os. You can
>>> >> add it by inserting
>>> >>
>>> >>  #define HAVE_SYS_TIME_H
>>> >>
>>> >> at the very top of the file gmxlib/thread_mpi/impl.h
>>> >>
>>> >> Then the package will probably compile and link, but
>>> >> mdrun's thread-mpi (tMPI) will not work on Cygwin
>>> >> (didn't work last time I tried).
>>> >>
>>> >> So you could do the following: 1) install the Gromacs
>>> >> package with "normal" compilation, and 2) build and
>>> >> install the openmpi-version of mdrun (mdrun_mpi).
>>> >>
>>> >> (1) cmake-options for package:
>>> >> ...
>>> >>       -DGMX_GPU=OFF                         \
>>> >>       -DGMX_PREFER_STATIC_LIBS=ON           \
>>> >> ...
>>> >>
>>> >> make -j4 install
>>> >>
>>> >> (delete all files from the build path)
>>> >>
>>> >> (2) cmake options for mdrun_mpi
>>> >> ...
>>> >>       -DGMX_GPU=OFF                        \
>>> >>       -DGMX_MPI=ON                         \
>>> >>       -DGMX_PREFER_STATIC_LIBS=ON          \
>>> >> ...
>>> >>
>>> >> make -j4 install-mdrun
>>> >>
>>> >> The openmpi-version (mdrun_mpi) runs reasonable on
>>> >> Cygwin/64 1.7.25, but not as fast as the native
>>> >> windows version (compiled with visual studio 10 or 12).
>>> >> The windows-compiled version of 4.6.3 is very robust and
>>> >> allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12)
>>> >> for unknown reasons). Then, you'll have full gpu support
>>> >> under windows.
>>> >>
>>> >> Regards
>>> >>
>>> >> M.
>>> >>
>>> >> --
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>>
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